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Merge pull request #31 from diffpy/update-objcryst-upstream-sync
Sync objcryst upstream and add standalone unit-test workflow
2 parents ed4fc9c + 3935a96 commit 2e5fd3d

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‎.github/workflows/unit-tests.yml‎

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name: Unit tests
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on:
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pull_request:
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workflow_dispatch:
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concurrency:
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group: unit-tests-${{ github.ref }}
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cancel-in-progress: true
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jobs:
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unit-tests:
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strategy:
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fail-fast: false
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matrix:
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include:
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- label: ubuntu-x64
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os: ubuntu-latest
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arch: x64
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make_cmd: make
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- label: macos-arm64
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os: macos-14
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arch: arm64
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make_cmd: gmake
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runs-on: ${{ matrix.os }}
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timeout-minutes: 45
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name: ${{ matrix.label }}
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steps:
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- name: Checkout repository
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uses: actions/checkout@v4
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with:
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fetch-depth: 0
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submodules: recursive
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- name: Set up Miniconda
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uses: conda-incubator/setup-miniconda@v3
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with:
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activate-environment: test-env
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auto-activate-base: false
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python-version: "3.13"
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- name: Install build dependencies (Ubuntu)
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if: startsWith(matrix.os, 'ubuntu-')
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shell: bash -el {0}
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run: |
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conda install -y -c conda-forge scons compilers boost
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- name: Install build dependencies (macOS)
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if: startsWith(matrix.os, 'macos-')
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shell: bash -el {0}
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run: |
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brew install make
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conda install -y -c conda-forge scons compilers boost
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- name: Build libobjcryst
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shell: bash -el {0}
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run: |
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sed -i.bak '/if gfb != afb:/,+1d' site_scons/libobjcrystbuildutils.py
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PREFIX="$CONDA_PREFIX" python -m SCons -Q lib
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- name: Locate built library
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shell: bash -el {0}
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run: |
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libpath="$(find "$PWD/build" -type f \( -name 'libObjCryst.so' -o -name 'libObjCryst.dylib' \) | head -n 1)"
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if [ -z "$libpath" ]; then
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echo "No built libObjCryst library found under build/"
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exit 1
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fi
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echo "LIBOBJCRYST_PATH=$libpath" >> "$GITHUB_ENV"
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echo "Using LIBOBJCRYST_PATH=$libpath"
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- name: Run standalone unit tests
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shell: bash -el {0}
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run: |
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CONDA_PREFIX="$CONDA_PREFIX" ${{ matrix.make_cmd }} -C test LIBOBJCRYST="$LIBOBJCRYST_PATH"

‎.gitignore‎

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# source distribution tarball
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libobjcryst-*.tar.gz
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# standalone unit-test artifacts
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test/bin/
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test/obj/

‎CHANGELOG.md‎

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# Release notes
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## Version 2026.2.0, - 2026-08-07
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### Changed
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- sync objcryst submodule to upstream `vincefn/objcryst` commit `4091cd9`, including:
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- CIF parser robustness fix for truncated input
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- fix for single-crystal simulation crashes
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- refinement guards for missing data/phase and empty MonteCarloObj
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- libobjcryst standalone workflow to build and run the upstream non-GUI unit-test suite
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## Version 2026.1, - 2026-02-05
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### Changed

‎site_scons/fallback_version.py‎

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Update FALLBACK_VERSION when tagging a new release.
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'''
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FALLBACK_VERSION = '2026.1.post0'
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FALLBACK_VERSION = '2026.2.0.post0'

‎src/objcryst‎

Submodule objcryst updated 61 files

‎test/Makefile‎

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ROOT_DIR := $(abspath $(CURDIR)/..)
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OBJCRYST_TEST_DIR := $(ROOT_DIR)/src/objcryst/test
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UNIT_SRC_DIR := $(OBJCRYST_TEST_DIR)/unit
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BUILD ?= fast
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ARCH ?= $(shell uname -m)
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BUILD_DIR ?= $(ROOT_DIR)/build/$(BUILD)-$(ARCH)
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LIBOBJCRYST ?= $(firstword $(wildcard $(BUILD_DIR)/src/libObjCryst*.so) \
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$(wildcard $(BUILD_DIR)/src/libObjCryst*.dylib) \
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$(wildcard $(BUILD_DIR)/src/libObjCryst*.dll) \
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$(wildcard $(BUILD_DIR)/src/libObjCryst*.a) \
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$(wildcard $(BUILD_DIR)/libObjCryst*.so) \
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$(wildcard $(BUILD_DIR)/libObjCryst*.dylib) \
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$(wildcard $(BUILD_DIR)/libObjCryst*.dll) \
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$(wildcard $(BUILD_DIR)/libObjCryst*.a))
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BIN_DIR := $(CURDIR)/bin/$(BUILD)-$(ARCH)
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OBJ_DIR := $(CURDIR)/obj/$(BUILD)-$(ARCH)
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RUNNER := $(CURDIR)/run_unit_tests.sh
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TEST_RUNNER := $(CURDIR)/test_runner.sh
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RM ?= rm -f
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MKDIR_P ?= mkdir -p
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CXX ?= c++
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CXXFLAGS ?= -O2 -std=c++14
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CPPFLAGS += -DREAL=double \
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-I$(ROOT_DIR)/src \
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-I$(ROOT_DIR)/src/objcryst \
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-I$(ROOT_DIR)/src/objcryst/test/unit \
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-I$(BUILD_DIR)/src \
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-I$(BUILD_DIR)/src/objcryst \
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-I$(BUILD_DIR)/src/version \
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-I$(ROOT_DIR)/src/objcryst/ObjCryst \
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-I$(ROOT_DIR)/src/objcryst/cctbx/include
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LDFLAGS += -L$(abspath $(dir $(LIBOBJCRYST)))
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LDLIBS += $(abspath $(LIBOBJCRYST))
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ifeq ($(origin CONDA_PREFIX), undefined)
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CONDA_PREFIX :=
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endif
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ifeq ($(shell uname -s),Darwin)
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RPATH_FLAG = -Wl,-rpath,$(dir $(LIBOBJCRYST))
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ifneq ($(strip $(CONDA_PREFIX)),)
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RPATH_FLAG += -Wl,-rpath,$(CONDA_PREFIX)/lib
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endif
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else
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RPATH_FLAG = -Wl,-rpath,$(dir $(LIBOBJCRYST))
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endif
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UNIT_TESTS := unit_cell_smoke crystallography_workflow \
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api_spacegroup api_crystal api_molecule api_scattering \
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api_powderpattern api_cif api_optimization api_indexing \
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ground_truth
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UNIT_BINS := $(addprefix $(BIN_DIR)/,$(UNIT_TESTS))
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UNIT_OBJS := $(addprefix $(OBJ_DIR)/,$(addsuffix .o,$(UNIT_TESTS)))
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.SECONDARY: $(UNIT_OBJS)
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.PHONY: all build run clean tidy check-layout
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all: build run
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build: check-layout $(UNIT_BINS) $(RUNNER)
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run: build $(RUNNER)
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@cd $(UNIT_SRC_DIR) && TEST_TIMEOUT="$${FOX_TEST_TIMEOUT:-30s}" BUILD="$(BUILD)" "$(RUNNER)"
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check-layout:
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@test -d "$(UNIT_SRC_DIR)" || { echo "Missing upstream unit test sources at $(UNIT_SRC_DIR)"; exit 1; }
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@test -f "$(TEST_RUNNER)" || { echo "Missing shared test runner at $(TEST_RUNNER)"; exit 1; }
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@test -n "$(LIBOBJCRYST)" || { echo "No built libObjCryst found under $(BUILD_DIR). Build libobjcryst first."; exit 1; }
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@test -f "$(ROOT_DIR)/src/objcryst/test/data/cif/PbSO4-COD-1528837.cif" || { echo "Missing required test data in src/objcryst/test/data"; exit 1; }
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$(BIN_DIR) $(OBJ_DIR):
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@$(MKDIR_P) "$@"
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$(OBJ_DIR)/%.o: $(UNIT_SRC_DIR)/%.cpp | $(OBJ_DIR)
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$(CXX) $(CPPFLAGS) $(CXXFLAGS) -c $< -o $@
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$(BIN_DIR)/%: $(OBJ_DIR)/%.o | $(BIN_DIR)
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$(CXX) $(CXXFLAGS) $(LDFLAGS) $(RPATH_FLAG) $< -o $@ $(LDLIBS)
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$(RUNNER):
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@chmod +x "$(RUNNER)"
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tidy:
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@$(RM) $(UNIT_OBJS)
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clean: tidy
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@$(RM) $(UNIT_BINS) "$(RUNNER)"

‎test/README.md‎

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This directory provides an independent unit-test harness for running the
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upstream ObjCryst non-GUI unit tests against the libobjcryst library built in
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this repository.
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Usage:
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1. Build libobjcryst in-tree with SCons, for example:
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`PREFIX=/path/to/env python -m SCons -Q lib`
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2. Build and run the unit tests:
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`CONDA_PREFIX=/path/to/env make -C test`
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The makefile expects the library under `build/<build>-<arch>/src/` and uses
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`build=fast` by default. Override `BUILD_DIR`, `BUILD`, `ARCH`, or `LIBOBJCRYST`
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when using a different in-tree layout.
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On macOS with a conda toolchain, pass `CONDA_PREFIX` so the test binaries add
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the environment runtime library directory to their rpath.

‎test/run_unit_tests.sh‎

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#!/usr/bin/env bash
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set -eu
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SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
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BIN_SUBDIR="${BUILD:-fast}-$(uname -m)"
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# shellcheck source=/dev/null
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. "$SCRIPT_DIR/test_runner.sh"
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TEST_TIMEOUT="${FOX_TEST_TIMEOUT:-30s}"
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run_test "unit::unit_cell_smoke" "$SCRIPT_DIR/bin/$BIN_SUBDIR/unit_cell_smoke"
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run_test "unit::crystallography_workflow" "$SCRIPT_DIR/bin/$BIN_SUBDIR/crystallography_workflow"
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run_test "unit::spacegroup" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_spacegroup" "spacegroup"
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run_test "unit::spacegroup-alternate-settings" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_spacegroup" "spacegroup-alternate-settings"
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run_test "unit::spacegroup-reflection-properties" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_spacegroup" "spacegroup-reflection-properties"
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run_test "unit::spacegroup-symmetry-operations" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_spacegroup" "spacegroup-symmetry-operations"
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run_test "unit::spacegroup-asymmetric-unit" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_spacegroup" "spacegroup-asymmetric-unit"
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run_test "unit::scattering-power-atom" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_crystal" "scattering-power-atom"
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run_test "unit::crystal-atom" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_crystal" "crystal-atom"
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run_test "unit::crystal-scatterer-management" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_crystal" "crystal-scatterer-management"
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run_test "unit::unitcell-geometry" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_crystal" "unitcell-geometry"
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run_test "unit::molecule-atoms-bonds" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_molecule" "molecule-atoms-bonds"
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run_test "unit::molecule-angles-dihedrals" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_molecule" "molecule-angles-dihedrals"
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run_test "unit::molecule-formula-loglikelihood" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_molecule" "molecule-formula-loglikelihood"
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run_test "unit::scatteringdata-singlecrystal" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_scattering" "scatteringdata-singlecrystal"
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run_test "unit::scatteringdata-radiation-types" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_scattering" "scatteringdata-radiation-types"
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run_test "unit::diffractiondata-observed" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_scattering" "diffractiondata-observed"
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run_test "unit::singlecrystal-groundtruth-xray" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_scattering" "singlecrystal-groundtruth-xray"
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run_test "unit::singlecrystal-groundtruth-neutron" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_scattering" "singlecrystal-groundtruth-neutron"
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run_test "unit::singlecrystal-simulate-ungrouped" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_scattering" "singlecrystal-simulate-ungrouped"
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run_test "unit::singlecrystal-simulate-grouped-equal" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_scattering" "singlecrystal-simulate-grouped-equal"
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run_test "unit::singlecrystal-simulate-grouped-user" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_scattering" "singlecrystal-simulate-grouped-user"
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run_test "unit::cif-import" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_cif" "cif-import"
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run_test "unit::cif-data-fields" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_cif" "cif-data-fields"
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run_test "unit::cif-coordinate-conversion" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_cif" "cif-coordinate-conversion"
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run_test "unit::cif-truncated-values" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_cif" "cif-truncated-values"
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run_test "unit::refinablepar" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_optimization" "refinablepar"
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run_test "unit::refinableobj" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_optimization" "refinableobj"
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run_test "unit::optimizationobj" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_optimization" "optimizationobj"
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run_test "unit::optimizationobj-limits-options" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_optimization" "optimizationobj-limits-options"
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run_test "unit::lsqnumobj" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_optimization" "lsqnumobj"
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run_test "unit::lsqnumobj-residual-statistics" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_optimization" "lsqnumobj-residual-statistics"
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run_test "unit::peaklist-simulate-volume" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_indexing" "peaklist-simulate-volume"
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run_test "unit::peaklist-add-remove" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_indexing" "peaklist-add-remove"
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run_test "unit::cellexplorer" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_indexing" "cellexplorer"
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run_test "unit::cellexplorer-configuration" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_indexing" "cellexplorer-configuration"
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run_test "unit::cellexplorer-dicvol-tetragonal" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_indexing" "cellexplorer-dicvol-tetragonal"
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run_test "unit::cellexplorer-dicvol-monoclinic" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_indexing" "cellexplorer-dicvol-monoclinic"
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run_test "unit::powderpattern-background" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_powderpattern" "powderpattern-background"
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run_test "unit::powderpattern-diffraction" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_powderpattern" "powderpattern-diffraction"
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run_test "unit::powderpattern-diffraction-mur" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_powderpattern" "powderpattern-diffraction-mur"
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run_test "unit::powderpattern-diffraction-lebail-fhklobs" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_powderpattern" "powderpattern-diffraction-lebail-fhklobs"
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run_test "unit::powderpattern-import" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_powderpattern" "powderpattern-import"
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run_test "unit::scatteringcorr-subclasses" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_powderpattern" "scatteringcorr-subclasses"
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run_test "unit::reflectionprofile-pseudo-voigt" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_powderpattern" "reflectionprofile-pseudo-voigt"
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run_test "unit::reflectionprofile-double-exponential-pv" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_powderpattern" "reflectionprofile-double-exponential-pv"
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run_test "unit::powder-groundtruth-xray-pv-gaussian" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_powderpattern" "powder-groundtruth-xray-pv-gaussian"
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run_test "unit::powder-groundtruth-xray-pv-lorentzian" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_powderpattern" "powder-groundtruth-xray-pv-lorentzian"
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run_test "unit::reflectionprofile-pv-anisotropic-direct" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_powderpattern" "reflectionprofile-pv-anisotropic-direct"
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run_test "unit::powder-groundtruth-xray-anisotropic" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_powderpattern" "powder-groundtruth-xray-anisotropic"
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run_test "unit::powder-groundtruth-neutron-pv-gaussian" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_powderpattern" "powder-groundtruth-neutron-pv-gaussian"
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run_test "unit::powder-groundtruth-neutron-pv-lorentzian" "$SCRIPT_DIR/bin/$BIN_SUBDIR/api_powderpattern" "powder-groundtruth-neutron-pv-lorentzian"

‎test/test_runner.sh‎

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#!/usr/bin/env bash
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set -eu
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SCRIPT_DIR="$(cd "$(dirname "$0")" && pwd)"
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ROOT_DIR="$(cd "$SCRIPT_DIR/.." && pwd)"
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# shellcheck source=/dev/null
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. "$ROOT_DIR/src/objcryst/test/scripts/test_runner.sh"

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